Using a network installation of WP modifies the media uploads URL structure to be that of http://example.com/files/2009/05/filename.jpg
Enabling a CDN then adds a subdomain to that URL. The problem with that is that since that URL is virtual WordPress can't find the file in the physical location and so it does what a network installation does and checks the subdomain for an existing site. It can't find it so it sends you to the wp-signup.php page and tells you that you can/cannot create a new site with that subdomain.
So the issue seems to be that W3TC should modify the htaccess to override WP's attempt at finding cdn.example.com
Any ideas on how to implement this now?